The complete chloroplast genomes of three Alismataceae species, including the medicinally important Alisma orientale

Figures & data

Figure 1. Herbarium specimens used in the Alisma chloroplast genome analyses. All three specimens show complete stems, leaves, inflorescences, flowers, and the detailed information of collection and identification. Images of (A) A. orientale and (B) A. subcordatum are from the official website of the US National Herbarium (https://collections.nmnh.si.edu/search/botany/), and the use of the photos and specimens has been authorized by the Curator, Dr. Jun Wen; and (C) A. triviale from the official website of the Kathryn Kalmbach Herbarium of the Denver Botanic Gardens (https://swbiodiversity.org/seinet/collections/harvestparams.php), and the use of the photos and specimens has been authorized by the Curator Dr. Jennifer Ackerfield.

Figure 2. The chloroplast genome map of (A) A. orientale, (B) A. subcordatum, and (C) A. triviale. The map was generated by CPGView. Genes located on the inner and outer of circle are transcribed clockwise and anticlockwise, respectively. The dark grey inner circle indicates GC content. Large single-copy (LSC), small single-copy (SSC), and inverted repeats (IRA and IRB) are indicated in the inner layer. The functional classification of the genes is provided in the bottom left corner.

Figure 3. Maximum-likelihood (ML) phylogenetic tree of the order Alismatales based on the complete cp genomes of 18 species in the order, with Dioscorea biformifolia (Dioscoreaceae) as the outgroup. The scale bar represents the number of substitutions per site. The bootstrap method used was SH-aLRT. The number above the line represents ML bootstrap value. The specie names colored in red represent the three newly sequenced chloroplast genomes (Alisma orientale OR773541, A. subcordatum OR773542 and A. triviale OR773543). The following sequences were used: Dioscorea biformifolia NC_077569 (unpublished), Tofieldia thibetica NC_029813 and Sagittaria lichuanensis NC_029815 (Luo et al. 2016), Wolffia australiana JN160605 (Wang and Messing 2011), Lemna minor NC_010109 (Mardanov et al. 2008), Zostera nigricaulis OR538605 (unpublished), Phyllospadix iwatensis NC_058622 (Chen et al. 2021), Butomus umbellatus NC_051949 (Yang and Liu 2019), Najas flexilis JX978472 (Peredo et al. 2013), Ottelia alismoides NC_057494 (Guo et al. 2020), Elodea canadensis JQ310743 (Huotari and Korpelainen 2012), Alisma plantago-aquatica NC_044108 and Sagittaria trifolia NC_044119 (Liang et al. 2019), Sagittaria graminea NC_067603 (unpublished), and Caldesia parnassifolia NC_045926 and C. grandis NC_045925 (Mwanzia et al. 2019).

Luo Y, Ma PF, Li HT, Yang JB, Wang H, Li DZ. 2016. Plastid phylogenomic analyses resolve Tofieldiaceae as the root of the early diverging monocot order Alismatales. Genome Biol Evol. 8(3):932–945. doi:10.1093/gbe/evv260.

 PubMed Web of Science ®Google Scholar

Wang W, Messing J. 2011. High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLOS One. 6(9):e24670. doi:10.1371/journal.pone.0024670.

 PubMed Web of Science ®Google Scholar

Mardanov AV, Ravin NV, Kuznetsov BB, Samigullin TH, Antonov AS, Kolganova TV, Skyabin KG. 2008. Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms. J Mol Evol. 66(6):555–564. doi:10.1007/s00239-008-9091-7.

 PubMed Web of Science ®Google Scholar

Chen J, Zang Y, Shang S, Liang S, Zhu M, Wang Y, Tang X. 2021. Comparative chloroplast genomes of Zosteraceae species provide adaptive evolution insights into seagrass. Front Plant Sci. 12:741152. doi:10.3389/fpls.2021.741152.

 PubMed Web of Science ®Google Scholar

Yang Z, Liu L. 2019. The complete chloroplast genome of Butomus umbellatus L. and its phylogenetic position. Mitochondrial DNA B Resour. 4(2):3700–3701. doi:10.1080/23802359.2019.1678435.

 PubMed Web of Science ®Google Scholar

Peredo EL, King UM, Les DH. 2013. The plastid genome of Najas flexilis: adaptation to submersed environments is accompanied by the complete loss of the NDH complex in an aquatic angiosperm. PLOS One. 8(7):e68591. doi:10.1371/journal.pone.0068591.

 PubMed Web of Science ®Google Scholar

Guo JL, Yu YH, Zhang YH. 2020. Characterization of the complete chloroplast genome of Ottelia alismoides (Hydrocharitaceae), a vulnerable submerged macrophyte in China. Mitochondrial DNA B Resour. 5(1):404–405. doi:10.1080/23802359.2019.1704197.

 PubMed Web of Science ®Google Scholar

Huotari T, Korpelainen H. 2012. Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes. Gene. 508(1):96–105. doi:10.1016/j.gene.2012.07.020.

 PubMed Web of Science ®Google Scholar

Liang JY, Ma Q, Yang ZP. 2019. The first complete chloroplast genomes of two Alismataceae species, and the phylogenetic relationship under order Alismatales. Mitochondrial DNA Part B. 4(1):122–123. doi:10.1080/23802359.2018.1536486.

 Web of Science ®Google Scholar

Mwanzia VM, Nzei JM, Yan DY, Kamau PW, Chen JM, Li ZZ. 2019. The complete chloroplast genomes of two species in threatened monocot genus Caldesia in China. Genetica. 147(5–6):381–390. doi:10.1007/s10709-019-00079-x.

 PubMed Web of Science ®Google Scholar

Data availability statement

The authors have deposited all the raw data in GenBank, which have all been activated. The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/ under the accession number OR773541, OR773542, and OR773543. The associated BioProject, SRA, and BioSample numbers are PRJNA1037010, SRX22416385 (Alisma orientale), SRX22416386 (Alisma subcordatum), SRX22416387 (Alisma triviale) and SAMN38155281 (Alisma orientale), SAMN38155282 (Alisma subcordatum), SAMN38155283 (Alisma triviale), respectively.